I have, however found an issue: after quitting the game and reloading from a save, Jump Drives and Tarsus Mk 2s are not available to purchase at any ship dealers in the system you saved in. I suspect this may have to do with the fact that these items have to be unlocked through a series of missions before they can be purchased, and somehow, this info is not being saved or loaded properly.

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Probably you're right. Needs some digging as to what variables are saved. Loading is not a problem - if you know what to check, it can be checked right in a base's python script.Of course, it's possible to introduce a virtual faction and set relations with it. But that's clumsy.